Early in the 2000's one of the original authors of Sfarflight posted a massive dump of information online: design documents and source code. That is the "Technical Articles Saved from Oblivion" link in this repository. Sadly no one seems to have managed to save a full copy! This is one I kick myself about: I browsed this back when it was up but didnt think to download. These days I make a point to request Internet Archives to save things like this if I ever come across it.

About halfway through my reverse-engineering process, I came across those documents and realized that roughly 50% were missing. I searched pretty much the entire web to see if anyone had stored these files elsewhere, but so far I haven’t had any luck.

I'm not sure what you're referring to since the files T.C. Lee posted on that geocities site are the only design documents he (or anyone else) ever released, and those are preserved in the SFFiles.zip found at the oocities mirror linked from the github there. That zip contained only a partial dump of some source code, while that sonic.net page contains a more complete copy (but lacks any kind of design documents whatsoever). Was there something else you were referring to?